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- PDB-6x3a: Crystal structure of the FN4-FN6 domains of human PTPRD -

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Basic information

Entry
Database: PDB / ID: 6x3a
TitleCrystal structure of the FN4-FN6 domains of human PTPRD
ComponentsReceptor-type tyrosine-protein phosphatase delta
KeywordsCELL ADHESION / Fibronectin type III / Receptor protein tyrosine phosphatase
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / synaptic membrane adhesion / regulation of postsynaptic density assembly / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / synaptic membrane adhesion / regulation of postsynaptic density assembly / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / phosphate-containing compound metabolic process / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / presynaptic membrane / receptor complex / signaling receptor binding / glutamatergic synapse / extracellular exosome / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBouyain, S. / Kawakami, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21AR066264 United States
CitationJournal: Plos One / Year: 2022
Title: Complex protein interactions mediate Drosophila Lar function in muscle tissue.
Authors: Kawakami, J. / Brooks, D. / Zalmai, R. / Hartson, S.D. / Bouyain, S. / Geisbrecht, E.R.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9642
Polymers34,8721
Non-polymers921
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.060, 34.570, 109.199
Angle α, β, γ (deg.)90.000, 90.334, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1395-

HOH

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 34872.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRD / Production host: Escherichia coli (E. coli) / References: UniProt: P23468, protein-tyrosine-phosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM Magnesium formate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 35136 / % possible obs: 99.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Net I/σ(I): 13.5
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1959 / CC1/2: 0.696 / Rpim(I) all: 0.453 / Rrim(I) all: 0.818

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Processing

Software
NameVersionClassification
PHENIXphasing
PHENIX1.18.1_3865refinement
MOSFLMdata reduction
Aimlessdata scaling
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dlar FN5

Resolution: 1.77→34.06 Å / SU ML: 0.2297 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1997 5.68 %
Rwork0.195 33136 -
obs0.1975 35133 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.99 Å2
Refinement stepCycle: LAST / Resolution: 1.77→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 6 312 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652499
X-RAY DIFFRACTIONf_angle_d0.82433411
X-RAY DIFFRACTIONf_chiral_restr0.0562380
X-RAY DIFFRACTIONf_plane_restr0.006445
X-RAY DIFFRACTIONf_dihedral_angle_d14.4398953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.33441410.29532342X-RAY DIFFRACTION98.45
1.81-1.860.27841380.26052302X-RAY DIFFRACTION98.79
1.86-1.910.28861440.25022353X-RAY DIFFRACTION98.93
1.91-1.980.34291390.22832321X-RAY DIFFRACTION98.95
1.98-2.050.30171410.23512338X-RAY DIFFRACTION99.08
2.05-2.130.29871450.22542343X-RAY DIFFRACTION99.32
2.13-2.230.28171400.22222346X-RAY DIFFRACTION99.4
2.23-2.340.26811440.21022375X-RAY DIFFRACTION99.41
2.34-2.490.2371390.20642361X-RAY DIFFRACTION99.56
2.49-2.680.2441430.21262373X-RAY DIFFRACTION99.53
2.68-2.950.22671420.19892375X-RAY DIFFRACTION99.64
2.95-3.380.20741420.182395X-RAY DIFFRACTION99.96
3.38-4.260.21341470.16732424X-RAY DIFFRACTION100
4.26-34.060.20091520.15722488X-RAY DIFFRACTION99.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.918088749990.492157527042-0.9233099753622.975349506130.4555497905093.69951702914-0.341662863850.234812794616-0.184509725097-0.245050869596-0.05075169717690.534231832121-0.120845382078-0.6930388416140.2841024859540.2006146920220.0487295338367-0.01671350963850.220661802766-0.06827775758050.2732581559620.95335790520821.731471387536.2273359282
26.92416967460.13782367452-0.1762445552242.306743672730.3588750308173.18336405914-0.5138616666011.12268087795-0.461630464283-0.4049477837010.1882825647480.128581765755-0.125153426738-0.4133055748070.2797471495570.287793147161-0.03901888361120.03344743088730.251077527775-0.08108869163480.2071808071358.1903111221421.375607009829.4415011998
35.344159272460.1125799705291.24686953482-0.03590645028090.2537454665271.84885573082-0.3919784290231.21445655878-0.1763470576630.1218606594070.178180852808-0.0367879642157-0.6670290054860.9906167800620.1698955057980.244276444701-0.15316743194-0.05753527500170.628625296096-0.009304184842480.22526099905945.758141881321.612266972941.2808006182
48.95918641245-0.1382577999021.321449448451.19108027072-0.5301981181516.86193811182-0.632044559020.168831582349-0.4030073999440.06667782278430.196072333560.161537897476-0.9674032862790.04935144984460.2659870442270.321163820844-0.0491045570614-0.03611409940840.373300614663-0.01170540694350.22973718874241.765661280921.727910906949.3693753266
54.699327369220.499355422152.011852627450.6685762064190.06633751637532.04934708488-0.5473257685911.12264381195-0.04706605608160.1256063576960.438123349158-0.0199887097941-0.5658051188020.6429015722060.132570304480.23514910163-0.103863791184-0.04834750929960.599215308885-0.07263068520370.24823833308548.728781825421.184644105644.1532086001
64.17918160680.1904934665330.08526998375493.627689905691.05893160445.560106464520.1121047701130.1577564032940.06149198477840.0901103366168-0.102009490528-0.0715968416009-0.333390861241-0.130978884341-0.02097582503330.174297463478-0.0285427719243-0.003427244341560.1048905186190.005326350038640.13921069239284.831843236431.954267620961.4878373841
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 610 through 640 )610 - 6401 - 33
22chain 'A' and (resid 641 through 708 )641 - 70834 - 104
33chain 'A' and (resid 709 through 758 )709 - 758105 - 156
44chain 'A' and (resid 759 through 776 )759 - 776157 - 174
55chain 'A' and (resid 777 through 822 )777 - 822175 - 220
66chain 'A' and (resid 823 through 915 )823 - 915221 - 317

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